I think you're trying to read too much into the story. The narrator simply describes Emily's father as sitting "spraddled" with his back to Emily and "clutching a horsewhip." We're never given any indication that he was physically abusive to her. Yes, we can speculate about their relationship and imagine all sorts of scenarios. We can also speculate just as well that the whip was to keep outsiders away. Remember that the narrator says, "None of the young men were quite good enough for Miss Emily." When she is still unmarried at 30 years of age when her father dies, the narrator says that surely she wouldn't have turned down a proposal if she had ever received one. Add to that the fact that she has her first gentleman friend after her father's death, and we can easily say that the whip was certainly a tool to keep men away from his precious daughter.